6-110506679-C-T

Variant names:

• chr6-110506679-C-T
• rs9481083

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.272 in 152,080 control chromosomes in the GnomAD database, including 6,357 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.27 (6357 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.78

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.384 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.272 AC: 41342 AN: 151962 Hom.: 6345 Cov.: 32

Gnomad AFR AF: 0.389

Gnomad AMI AF: 0.292

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.401

Gnomad EAS AF: 0.00173

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.157

Gnomad MID AF: 0.411

Gnomad NFE AF: 0.253

Gnomad OTH AF: 0.290

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.272 AC: 41379 AN: 152080 Hom.: 6357 Cov.: 32 AF XY: 0.263 AC XY: 19531 AN XY: 74330

Gnomad4 AFR AF: 0.389

Gnomad4 AMR AF: 0.222

Gnomad4 ASJ AF: 0.401

Gnomad4 EAS AF: 0.00174

Gnomad4 SAS AF: 0.133

Gnomad4 FIN AF: 0.157

Gnomad4 NFE AF: 0.253

Gnomad4 OTH AF: 0.286

Alfa AF: 0.260 Hom.: 3813

Bravo AF: 0.286

Asia WGS AF: 0.0940 AC: 327 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.44
DANN	Benign	0.52

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs9481083; hg19: chr6-110827882;